Infants with inborn errors of bile acid metabolism represent a relatively heterogeneous group of patients with a variety of clinical manifestations. They can range from neonatal cholestasis and severe liver injury in the neonate to fat-soluble vitamin deficiency and its manifestations in the older child or even end stage cirrhosis in later childhood. In addition, defects of peroxisomal metabolism of bile acids may be manifest as in peroxisomal disorders such as Zellweger syndrome or infantile adrenoleukodystrophy. Using techniques of mass spectrometry including fast atom bombardment on urine samples, electron microscopy and MRI-spectroscopy, we have evaluated a growing group of infants and children with these disorders.